Project name: 86e9d7334d5a30e [mutate: IV76A]

Status: done

Started: 2020-04-05 16:21:42
Settings
Chain sequence(s) A: QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNAWVFGGGTKLTVLG
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues IV76A
Energy difference between WT (input) and mutated protein (by FoldX) 1.19549 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:00:44)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:45)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:07)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:16:30)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:16:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:16:33)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:16:33)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:16:33)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:16:34)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:16:34)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:16:36)
[INFO]       Movie:    Creting movie with webm format                                              (00:17:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:49)
Show buried residues
Minimal score value
-2.5613
Maximal score value
1.8784
Average score
-0.5456
Total score value
-60.5645
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 Q A -0.8362
2 S A 0.2824
3 V A 1.6407
4 L A 0.0000
5 T A 0.0613
6 Q A 0.0000
7 P A -0.7117
8 P A -1.0077
9 S A -1.0666
10 A A -0.6852
11 S A -0.4963
12 G A 0.0000
13 T A -0.4846
14 P A -1.0973
15 G A -1.7551
16 Q A -2.3701
17 R A -2.5613
18 V A -1.1585
19 T A -0.4925
20 I A 0.0000
21 S A -0.4000
22 C A 0.0000
23 S A -0.2898
24 G A -0.0289
25 S A -0.3414
26 S A -0.9486
27 S A -0.8380
28 N A 0.0000
29 I A 0.0000
30 G A -1.2705
31 S A -0.9639
32 N A -0.7755
33 T A -0.5679
34 V A 0.0000
35 N A 0.0159
36 W A 0.0000
37 Y A 0.1242
38 Q A 0.0000
39 Q A -0.6726
40 L A -0.1925
41 P A -0.2706
42 G A -0.4382
43 T A -0.3923
44 A A -0.4080
45 P A -0.7863
46 K A -1.1293
47 L A 0.1265
48 L A 0.0000
49 I A 0.0000
50 Y A -0.2187
51 S A -0.8739
52 N A -1.3854
53 N A -2.0737
54 Q A -1.7370
55 R A -1.7508
56 P A -0.8498
57 S A -0.7913
58 G A -0.7402
59 V A -0.9893
60 P A -1.3080
61 D A -2.2469
62 R A -1.6272
63 F A 0.0000
64 S A -1.3415
65 G A 0.0000
66 S A -1.2354
67 K A -1.4058
68 S A -0.9643
69 G A -1.0350
70 T A -0.9132
71 S A -0.8111
72 A A 0.0000
73 S A -0.6624
74 L A 0.0000
75 A A -0.5704
76 V A 0.0000 mutated: IV76A
77 S A -1.7370
78 G A -1.6787
79 L A 0.0000
80 Q A -1.7270
81 S A -1.5837
82 E A -2.2744
83 D A 0.0000
84 E A -1.6780
85 A A 0.0000
86 D A -1.0792
87 Y A 0.0000
88 Y A 0.0428
89 C A 0.0000
90 A A 0.0000
91 A A 0.0000
92 W A 0.6273
93 D A 0.0000
94 D A -1.4503
95 S A -0.5526
96 L A 0.6481
97 N A -0.7433
98 A A 0.5042
99 W A 1.7421
100 V A 0.0000
101 F A 1.8784
102 G A 0.0000
103 G A -0.4022
104 G A -0.5632
105 T A 0.0000
106 K A -2.1815
107 L A 0.0000
108 T A -0.7004
109 V A -0.3198
110 L A 1.1105
111 G A 0.2711
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.5456 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
input -0.5456 View CSV PDB
model_1 -0.5578 View CSV PDB
model_2 -0.5873 View CSV PDB
model_10 -0.6202 View CSV PDB
model_7 -0.6283 View CSV PDB
model_4 -0.6385 View CSV PDB
model_5 -0.6505 View CSV PDB
model_3 -0.6624 View CSV PDB
model_0 -0.6699 View CSV PDB
model_9 -0.673 View CSV PDB
model_6 -0.708 View CSV PDB
model_8 -0.7117 View CSV PDB
model_11 -0.7677 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018